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Research Summary

Quantifying and Characterizing Human-Microbiome Interactions

The Gilbert Lab is pioneering efforts to define how our microbial ecosystems evolve in both our built environments and our bodies. From the moment we are born all of our interactions with the world around us expose us to different sources of microbes that influence the trajectory of our microbial succession. Over the last 150 years we, as a species, have migrated to an indoor ecosystem that has been mostly isolated from the natural environments we evolved in. This is changing the array of microbial sources that we can call upon to construct our human microbiome. We are using traditional sampling and next generation sensor approaches to capture the microbial dynamics of indoor and outdoor built environments, so as to quantify and map the direction of microbial transmission between humans and the air and surfaces of these systems.

Mapping the global microbiome

Dr. Gilbert founded and has led the Earth Microbiome Project (www.earthmicrobiome.org) and American Gut (www.americangut.org), two massive collaborative efforts aimed at developing a comprehensive understanding of the bacterial and fungal communities that inhabit the myriad niches across our planet and in our bodies. The Earth Microbiome Project has worked with more than 200 collaborators around the world to characterize the bacterial assemblages in >30,000 ecosystems, creating the most comprehensive assessment of microbial ecosystems ever undertaken. These data are being used to map and extrapolate globally relevant ecosystem processes that are mediated by microbial biogeochemical activity. The crowd-funded American Gut project works with the public to facilitate the construction of a vast knowledge base to address human microbial diversity, with the future goal of creating translational impact on forensic and health outcomes.

Mapping and modeling microbial ecosystems

We leverage advanced modeling frameworks to capture the species distribution, and functional potential dynamics driven by physicochemical properties. We are developing techniques to include viral and eukaryotic dynamics into bacterial models to improve the predictability of ecosystem processes in marine, soil and human environments. Furthermore, we are innovating the use of genome-enabled metabolic models that capture the chemical cross-talk between bacteria and archaea in diverse ecosystems. These metabolic models have the potential to identify novel protein functions, providing an opportunity to focus on future biochemical exploration.